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Structural basis for monolignol oxidation by a maize laccase

Nature Plants volume 6, pages 231–237 (2020)Cite this article

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Abstract

Plant laccases catalyse the oxidation of monolignols in lignification, a process reinforcing the cell wall of many different cell types that provide mechanical support, nutrient transportation and defence against pathogens in plants1. The isozymes display a broad range of substrate preferences. Here, the substrate preference of a laccase (ZmLac3) from Zea mays (maize) was characterized. The crystal structure of ZmLac3 revealed a compact and deep substrate-binding pocket, and the binding modes of sinapyl alcohol (SinA) and coniferyl alcohol (ConA) were solved. On the basis of structural data and kinetics analysis, we propose that the regionalization of polar and hydrophobic surfaces in the binding pocket of ZmLac3 is vital for defining the orientation of SinA/ConA binding. The extra methoxyl group in SinA makes substantial contributions to interactions between SinA and ZmLac3, which are absent in the ZmLac3–ConA complex. In summary, the polar and hydrophobic interactions between SinA/ConA and ZmLac3 determine the binding positions of the monolignols in ZmLac3. These results provide valuable insight about ZmLac3 catalysis and should aid industrial processes that use plant laccases.

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Fig. 1: Overall structure of ZmLac3.
Fig. 2: SinA/ConA binding at the substrate pocket.

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Data availability

The atomic coordinates and structure factors have been deposited in the Protein Data Bank with accession codes 6KLG (ZmLac3 native), 6KLI (ZmLac3–SinA complex) and 6KLJ(ZmLac3–ConA complex).

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Acknowledgements

This work was supported by grants from the Innovative Academy of Seed Design (INASEED) at the Chinese Academy of Science, initial grants from the 100 Talents Program of the Chinese Academy of Sciences and the open fund from the Key Laboratory of Environmental and Applied Microbiology at the Chinese Academy of Sciences (grant nos. KLCAS-2016-09 and KLCAS-2017-05). We thank the Shanghai Synchrotron Radiation Facilities (SSRF) and the National Center for Protein Science Shanghai (NCPSS) for the provision of synchrotron radiation facilities and efficient support.

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Authors and Affiliations

  1. Key Laboratory of Environmental and Applied Microbiology, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China

    Tian Xie, Zhongchuan Liu & Ganggang Wang

  2. Key Laboratory of Environmental Microbiology of Sichuan Province, Chengdu, China

    Tian Xie, Zhongchuan Liu & Ganggang Wang

  3. The Innovative Academy of Seed Design (INASEED), Chinese Academy of Sciences, Beijing, China

    Ganggang Wang

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  1. Tian Xie
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Contributions

T.X., Z.L. and G.W. designed the research. T.X. expressed, purified and crystallized ZmLac3 and performed the biochemical assays. T.X. and Z.L. collected and processed the diffraction data. Z.L. determined the structures. T.X., Z.L. and G.W. wrote the manuscript. G.W. directed and supervised all of the research.

Corresponding author

Correspondence to Ganggang Wang.

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The authors declare no competing interests.

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Peer review information Nature Plants thanks Jane Agger, Kurt Fagerstedt and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1

Data collection and refinement statistics.

Extended Data Fig. 2 Topology structure of Zmlac3.

Sheets in domains I, II and III are coloured red, blue and green, respectively. Alpha-helices and 310 helices are shown as cyan and magenta cylinders, respectively. The figure was prepared by TopDraw software47.

Extended Data Fig. 3 Sequence alignment between zmlac3 and other plant laccases.

Similarities are depicted in grey-scale shading and residues that are identical indicated by a black background. Four substrate-binding loops are marked by blue boxes. Orange stars placed above the sequences indicate amino acids that may interact with substrates. 17 A. thaliana laccases (AtLacs)4, 5 Z. mays W64A laccases (ZmLacs)3, A.pseudoplatanus laccase (ApLac)48, Litchi chinensis laccase (LcLac)12, Gossypium arboretum laccase (GaLac)49, Gossypium hirsutum-15 (GhLac15)6, Saccharum officinarum laccase (SoLac)50, two P. taeda laccases (PtLacs)51, Populus euramericana laccase-90 (PeLac90)52 and Picea abies laccase-4 (PaLac4)53 were included in the alignment. The alignment was generated by ALINE54.

Extended Data Fig. 4

Statistics of three-dimensional alignment between Zmlac3 and various laccases55,56 by DALI57.

Extended Data Fig. 5

SAA, SAV and depth of substrate binding pockets in laccases.

Extended Data Fig. 6 Electron density map around SinA/ConA located in the binding pocket.

The 2Fo-Fc electron density map (1σ level, blue) and the omit Fo-Fc map (2σ level, red) around SinA (a) and ConA (b) in the binding pocket are represented in mesh.

Extended Data Fig. 7

Laccase candidates identified in maize B73. To explore the laccase candidates in Z. mays B73 genome (Refgen_V4)24, protein sequences of 17 AtLacs from A. thaliana and 5 ZmLacs from Z. mays WB64A were used as queries for BLASTP58 on Gramene59 online. The hits without three cupredoxin domains or copper binding sites were excluded. Then, the phylogenetic analysis of the candidate proteins with AtLacs, ZmLacs and plant ascorbate oxidases60 was performed in MEGA software (http://www.megasoftware.net). The hits clustered with plant ascorbate oxidases were discarded. Finally, a total of 19 laccase candidates (Gene IDs in Gramene59 and MaizeGDB61 are listed) were found in Z. mays B73 genome, which showed 36–99% sequence identity to the counterparts in Z. mays WB64A (Extended Data Fig. 9).

Extended Data Fig. 8 Neighbor-joining phylogenetic analysis of Zmlac3 with other laccases in Maize W64A and B73.

The phylogenetic tree was constructed by MEGA software (http://www.megasoftware.net/) with bootstrap tests for 1,000 replicates. 10 AtLacs4, 5 ZmLacs3 and 19 predicted ZmLacs_B73 (Extended Data Fig. 7) were clustered into five groups.

Extended Data Fig. 9

Sequence identity of laccases in maize W64A and B73.

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Xie, T., Liu, Z. & Wang, G. Structural basis for monolignol oxidation by a maize laccase. Nat. Plants 6, 231–237 (2020). https://doi.org/10.1038/s41477-020-0595-5

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